Fig. 5.

Fold-critical E-values of the negative hits (in logarithm of 10) versus their corresponding false-positive rates (in logarithm of 10). At the recommended E-value cutoff of 0.1 (see vertical dotted line), the HMMER2 false-positive rate is lower (at 0.53) than that of HMMER3 (at 0.79). The equivalent HMMER3 E-value cutoff to achieve the same false-positive rate would have been 10^–3. Conversely, if a false-positive rate of 0.01 (see horizontal dotted line) is set, the corresponding HMMER2 and HMMER3 fold-critical E-value cutoffs corresponds to 10^–6 and 10^–9 respectively